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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTGATATTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtcatgggctatttttacatacacccacctcattggcccttatatcttactgatctttgaaactattataattatcagcttgatgtaagatatt...

Basic information

species Oryza sativa
transcript LOC_Os11g14950.1
intron # 10
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88305966|gb|CI634963.1|CI634963
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88490827|gb|CI428099.1|CI428099
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88333965|gb|CI645379.1|CI645379
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88851519|gb|CI670959.1|CI670959
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88475569|gb|CI412840.1|CI412840
EST:     ACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: ACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88480706|gb|CI417977.1|CI417977
EST:     CACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: CACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88476916|gb|CI414187.1|CI414187
EST:     GGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: GGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88347292|gb|CI632577.1|CI632577
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|33799625|gb|CF325673.1|CF325673
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88331000|gb|CI638408.1|CI638408
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|29637025|gb|CB642034.1|CB642034
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|218496146|gb|FG946660.1|FG946660
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATG
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATG
EST: gi|29642738|gb|CB647745.1|CB647745
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88334143|gb|CI641194.1|CI641194
EST:     TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: TTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
EST: gi|88281252|gb|CI402450.1|CI402450
EST:     CCGTAACTCTTCAG                         CTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC
genomic: CCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 60 (upstream exon), 61 (downstream exon)
Score: 22

GATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTGATATTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtca ... tggcatgcagCTTACTGGAGACCTTGATAAAATGGTCGCATTACAAAGGATGCTCGAGCCCTATGGCATTTGTGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTGCTGTAAACACCACAGCCCGCAGGGCTATCCTAGATATTGCTGATATTTTCCGGGCCAAAACTGTGGATGTATCAGATCACACCGTAACTCTTCAGgtaatagtcatgggctatttttacatacacccacctcattggcccttatatcttactgatctttgaaactattataattatcagcttgatgtaagatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacctc